If you add those files to the trusted list on the core your users will not get the popups. In 9.0 sp3 there is not automatic way to check the reputation of a file. You would have to update your core to 9.5 sp1 to be able to leverage the LANDesk file reputation service to accomplish that.
be honest, what kind of files will trigger the popups and we should add to the trusted list?
it seems so difficult to define which files should be added to trusted list.
Some users' PC will not trigger the popups but they also got such application.